scholarly journals Characterization of a Novel Ourmia-Like Mycovirus Infecting Magnaporthe oryzae and Implications for Viral Diversity and Evolution

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 223 ◽  
Author(s):  
Chang Li ◽  
Jun Zhu ◽  
Bi Gao ◽  
Hong Zhu ◽  
Qian Zhou ◽  
...  
Keyword(s):  
Magnaporthe Oryzae ◽  
Expressed Sequence Tag ◽  
Phytopathogenic Fungus ◽  
Mycelium Growth ◽  
Reading Frame ◽  
A Genome ◽  
Wide Range ◽  
Host Fungus ◽  
Shotgun Assembly

Here, the molecular characterization of a novel mycovirus that was isolated from a phytopathogenic fungus Magnaporthe oryzae and designed as Magnaporthe oryzae ourmia-like virus 4 (MOLV4) is reported. MOLV4 has a genome that is 2497 bp long and possesses a single open reading frame (ORF), which encodes the product RNA-dependent RNA polymerase (RdRp). Sequence similarities were found between the MOLV4 encoded RdRp and the counterparts of a few previously reported ourmia-like mycoviruses. Virus-curing and biological comparison indicate that the virus has no or mild effects on the morphology and mycelium growth rate of the host fungus. Phylogenetic analysis using the RdRp aa sequences was performed. The results show that MOLV4 is clustered with the ourmia-like mycoviruses, forming a clade closely related to ourmiaviruses but distinct from narnaviruses. In addition, database searches revealed that several MOLV4-related sequences are present in the transcriptome shotgun assembly (TSA) library, expressed sequence tag database (ESTdb), whole-genome shotgun (WGS) library, and genomic survey sequences (GSS) libraries of a few other species of eukaryote organisms. Our results show that MOLV4, together with other similar ourmia-like mycoviruses, might represent a virus clade that links the plant ourmiaviruses and fungal narnaviruses and has a wide range of hosts.

Cloning, expression and characterization of NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase of adult Haemonchus contortus†

2010 ◽  
Vol 85 (4) ◽  
pp. 421-429 ◽  
Author(s):  
K. Han ◽  
L. Xu ◽  
R. Yan ◽  
X. Song ◽  
X. Li
Keyword(s):  
Enzymatic Activity ◽  
Haemonchus Contortus ◽  
Expressed Sequence Tag ◽  
Sequence Similarity ◽  
Full Length ◽  
Amino Acid Residues ◽  
Gapdh Gene ◽  
Wide Range ◽  
Rapid Amplification

AbstractGlyceraldehyde-3-phosphate dehydrogenase (GAPDH) regulates a wide range of biological processes, including pathogen evasion. In the present research, the GAPDH gene of Haemonchus contortus (HcGAPDH) was cloned and characterized. Specific primers for the rapid amplification of cDNA ends (RACE) were designed based on the expressed sequence tag (EST, AW670737) to amplify the 3′ and 5′ ends of HcGAPDH. The full length of cDNA from this gene was obtained by overlapping the sequences of 3′ and 5′ extremities and amplification by reverse transcription polymerase chain reaction (RT-PCR). The biochemical activities of the recombinant protein HcGAPDH, which was expressed in prokaryotic cells and purified by affinity chromatography, were analysed by assays of enzymatic activity, thermal stability and pH. The results showed that the cloned full-length cDNA comprised 1303 bp and encoded a peptide with 341 amino acid residues which showed sequence similarity to several known GAPDHs. The biochemical assay showed that the protein encoded by the HcGAPDH exhibited enzymatic activity with NAD+ as a cofactor. HcGAPDH was stable between pH 5 and 9 and maintained activity at high temperatures of up to 75°C. The natural GAPDH of Haemonchus contortus detected by immunoblot assay was approximately 38 kDa in size, and the recombinant HcGAPDH was recognized strongly by serum from naturally infected goats.

scholarly journals A Highly Conserved Protein of Unknown Function Is Required by Sinorhizobium meliloti for Symbiosis and Environmental Stress Protection

2007 ◽  
Vol 190 (3) ◽  
pp. 1118-1123 ◽  
Author(s):  
Bryan W. Davies ◽  
Graham C. Walker
Keyword(s):  
Environmental Stress ◽  
Unknown Function ◽  
Sinorhizobium Meliloti ◽  
Environmental Stresses ◽  
Protein Family ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Stress Protection ◽  
Wide Range

ABSTRACT We report here the first characterization of the Sinorhizobium meliloti open reading frame SMc01113. The SMc01113 protein is a member of a highly conserved protein family, universal among bacteria. We demonstrate that the SMc01113 gene is absolutely required for S. meliloti symbiosis with alfalfa and also for the protection of the bacterium from a wide range of environmental stresses.

scholarly journals Complex Metabolic Phenotypes Caused by a Mutation in yjgF, Encoding a Member of the Highly Conserved YER057c/YjgF Family of Proteins

1998 ◽  
Vol 180 (24) ◽  
pp. 6519-6528 ◽  
Author(s):  
Jodi L. Enos-Berlage ◽  
Mark J. Langendorf ◽  
Diana M. Downs
Keyword(s):  
Pentose Phosphate Pathway ◽  
Biosynthetic Pathway ◽  
Genetic Characterization ◽  
Pentose Phosphate ◽  
Oxidative Pentose Phosphate Pathway ◽  
Phenotypic Characterization ◽  
Reading Frame ◽  
Wide Range ◽  
Isoleucine Biosynthesis

ABSTRACT The oxidative pentose phosphate pathway is required for function of the alternative pyrimidine biosynthetic pathway, a pathway that allows thiamine synthesis in the absence of the PurF enzyme inSalmonella typhimurium. Mutants that no longer required function of the oxidative pentose phosphate pathway for thiamine synthesis were isolated. Further phenotypic analyses of these mutants demonstrated that they were also sensitive to the presence of serine in the medium, suggesting a partial defect in isoleucine biosynthesis. Genetic characterization showed that these pleiotropic phenotypes were caused by null mutations in yjgF, a previously uncharacterized open reading frame encoding a hypothetical 13.5-kDa protein. The YjgF protein belongs to a class of proteins of unknown function that exhibit striking conservation across a wide range of organisms, from bacteria to humans. This work represents the first detailed phenotypic characterization of yjgF mutants in any organism and provides important clues as to the function of this highly conserved class of proteins. Results also suggest a connection between function of the isoleucine biosynthetic pathway and the requirement for the pentose phosphate pathway in thiamine synthesis.

scholarly journals Functional Characterization of a Catabolic Plasmid from Polychlorinated- Biphenyl-Degrading Rhodococcus sp. Strain RHA1

2004 ◽  
Vol 186 (22) ◽  
pp. 7783-7795 ◽  
Author(s):  
René Warren ◽  
William W. L. Hsiao ◽  
Hisashi Kudo ◽  
Matt Myhre ◽  
Manisha Dosanjh ◽  
...  
Keyword(s):  
Polychlorinated Biphenyl ◽  
Functional Characterization ◽  
Housekeeping Genes ◽  
Complete Sequence ◽  
Genomic Islands ◽  
Reading Frame ◽  
Sequencing Project ◽  
A Genome ◽  
Sequence Elements

ABSTRACT Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative “genomic islands” (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.

scholarly journals Identification and Characterization of a Novel Emaravirus From Grapevine Showing Chlorotic Mottling Symptoms

2021 ◽  
Vol 12 ◽  
Author(s):  
Xudong Fan ◽  
Chen Li ◽  
Zunping Zhang ◽  
Fang Ren ◽  
Guojun Hu ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
High Throughput Sequencing ◽  
Rna Virus ◽  
Reading Frame ◽  
A Genome ◽  
The Family ◽  
Pcr Products ◽  
Chlorotic Mottling

A novel negative-sense, single-stranded (ss) RNA virus was identified in a “Shennong Jinhuanghou” (SJ) grapevine showing severe chlorotic mottling symptoms by integrating high-throughput sequencing (HTS) and conventional Sanger sequencing of reverse transcription polymerase chain reaction (RT-PCR) products. The virus was provisionally named as “grapevine emaravirus A” (GEVA). GEVA had a genome comprising five genomic RNA segments, each containing a single open reading frame on the viral complementary strand and two untranslated regions with complementary 13- nt stretches at the 5′ and 3′ terminal ends. RNA1 (7,090 nt), RNA2 (2,097 nt), RNA3 (1,615 nt), and RNA4 (1,640 nt) encoded putative proteins P1–P4 that, based on their conserved motifs, were identified as the RNA-dependent RNA polymerase, glycoprotein, nucleocapsid protein, and movement protein, respectively. However, the functional role of protein P5 encoded by RNA5 (1,308 nt) could not be determined. Phylogenetic trees constructed based on amino acids of P1 to P4, allocated GEVA in clade I, together with other species-related emaraviruses. These data support the proposal that GEVA is a representative member of a novel species in the genus Emaravirus of the family Fimoviridae. Moreover, when GEVA was graft-transmitted to SJ and “Beta” grapevines, all grafted plants showed the same symptoms, similar to those observed in the source of the inoculum. This is the first report to our knowledge of an emaravirus infecting grapevine and its possible association with chlorotic mottling symptoms.

scholarly journals Cloning of a Novel Pyrethroid-Hydrolyzing Carboxylesterase Gene from Sphingobium sp. Strain JZ-1 and Characterization of the Gene Product

2009 ◽  
Vol 75 (17) ◽  
pp. 5496-5500 ◽  
Author(s):  
Bao-zhan Wang ◽  
Peng Guo ◽  
Bao-jian Hang ◽  
Lian Li ◽  
Jian He ◽  
...  
Keyword(s):  
Short Chain Fatty Acids ◽  
Nitrilotriacetic Acid ◽  
Reading Frame ◽  
Hydrolase Fold ◽  
Wide Range ◽  
Pyrethroid Pesticides ◽  
Novel Esterase ◽  
Esterase Gene ◽  
Monomeric Structure

ABSTRACT A novel esterase gene, pytH, encoding a pyrethroid-hydrolyzing carboxylesterase was cloned from Sphingobium sp. strain JZ-1. The gene contained an open reading frame of 840 bp. Sequence identity searches revealed that the deduced enzyme shared the highest similarity with many α/β-hydrolase fold proteins (20 to 24% identities). PytH was expressed in Escherichia coli BL21 and purified using Ni-nitrilotriacetic acid affinity chromatography. It was a monomeric structure with a molecular mass of approximately 31 kDa and a pI of 4.85. PytH was able to transform p-nitrophenyl esters of short-chain fatty acids and a wide range of pyrethroid pesticides, and isomer selectivity was not observed. No cofactors were required for enzyme activity.

scholarly journals Discovery and Characterization of a Novel Bipartite Botrexvirus From the Phytopathogenic Fungus Botryosphaeria dothidea

2021 ◽  
Vol 12 ◽  
Author(s):  
Mengmeng Yang ◽  
Wenxing Xu ◽  
Xiaoqi Zhou ◽  
Zuokun Yang ◽  
Yanxiang Wang ◽  
...  
Keyword(s):  
Biological Effects ◽  
Plant Viruses ◽  
Open Reading Frames ◽  
Phytopathogenic Fungus ◽  
Botryosphaeria Dothidea ◽  
Bipartite Genome ◽  
The Family ◽  
Host Fungus

In this study, we describe a novel positive, single-stranded (+ss) RNA mycovirus, named Botryosphaeria dothidea botrexvirus 1 (BdBV1), from a phytopathogenic fungus Botryosphaeria dothidea showing abnormal morphology and attenuated virulence. BdBV1 is phylogenetically related to Botrytis virus X (BotVX) and is the second potential member of the proposed genus Botrexvirus in the family Alphaflexiviridae. However, it differs from the monopartite BotVX in that BdBV1 possesses a bipartite genome comprised of two ssRNA segments (RNA1 and RNA2 with lengths of 5,035 and 1,063 nt, respectively). BdBV1 RNA1 and RNA2 encode putative RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes, which share significant identity with corresponding genes in both fungal and plant viruses. Moreover, open reading frames (ORFs) 2–4 of BdBV1 RNA1 shared no detectable identity with any known viral proteins. Immunosorbent electron microscopy (ISEM) analysis using an antibody against the virus CP generated in vitro revealed that BdBV1 is encapsidated in filamentous particles. A comparison of the biological effects of BdBV1 infection on symptoms and growth in isogenic lines of virus-free and virus-infected B. dothidea revealed that BdBV1 is probably involved in reduced growth and virulence of the host fungus. This study describes and characterizes a novel bipartite botrexvirus, which is closely related to uni- and multi-partite fungal and plant viruses and contributes useful information to a better understanding of virus evolution.

scholarly journals Molecular characterization of a novel polymycovirus from the phytopathogenic fungus Setosphaeria turcica

2021 ◽  
Author(s):  
Zhongnan Gao ◽  
Manyu Zhang ◽  
Tingting Yu ◽  
Xiaoyan Wang ◽  
Xin Wang ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Novel Species ◽  
Plasmopara Viticola ◽  
Phytopathogenic Fungus ◽  
Phylogeny Reconstruction ◽  
Setosphaeria Turcica ◽  
Sequence Identity ◽  
A Genome ◽  
The Family

Abstract A putative polymycovirus tentatively named Setosphaeria turcica polymycovirus 1 (StPmV1) was discovered from the phytopathogenic fungus Setosphaeria turcica. StPmV1 has a genome comprising 5 double stranded RNAs (dsRNAs). DsRNA1-3 each encodes a protein sharing significant but lower than 64% sequence identity with corresponding proteins from other polymycoviruses. DsRNA4-5 each encodes a protein with a sequence not conserved among polymycoviral proteins. However, the protein encoded by dsRNA4 is rich in proline (P), alanine (A), and serine (S) residues, which is a feature shared by the so-called PAS-rich proteins encoded by all polymycoviruses. Phylogeny reconstruction using the RNA-dependent RNA polymerases (RdRp) of accepted or putative polymycoviruses revealed that StPmV1 is most closely related to Plasmopara viticola lesion associated Polymycovirusmyco 1 (PvaPolymyco1), a putative polymycovirus recovered from the phytopathogenic oomycetes Plasmopara viticola. These data suggest that StPmV1 may represent a novel species of the genus Polymycovirus under the family Polymycoviridae. To our knowledge, this is the first polymycovirus reported from S. turcica.

scholarly journals A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data

2014 ◽  
Vol 2014 ◽  
pp. 1-11
Author(s):  
Yu Bai ◽  
Yuki Iwasaki ◽  
Shigehiko Kanaya ◽  
Yue Zhao ◽  
Toshimichi Ikemura
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Self Organizing Map ◽  
Genome Signature ◽  
A Genome ◽  
Wide Range ◽  
Oligonucleotide Composition ◽  
Species Specific

With remarkable increase of genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition on one map. By modifying the conventional SOM, we have previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, solely depending on the oligonucleotide composition. In the present study, we introduce the oligonucleotide BLSOM used for characterization of vertebrate genome sequences. We first analyzed pentanucleotide compositions in 100 kb sequences derived from a wide range of vertebrate genomes and then the compositions in the human and mouse genomes in order to investigate an efficient method for detecting differences between the closely related genomes. BLSOM can recognize the species-specific key combination of oligonucleotide frequencies in each genome, which is called a “genome signature,” and the specific regions specifically enriched in transcription-factor-binding sequences. Because the classification and visualization power is very high, BLSOM is an efficient powerful tool for extracting a wide range of information from massive amounts of genomic sequences (i.e., big sequence data).

scholarly journals Gaussian-distributed codon frequencies of genomes

2018 ◽  
Author(s):  
Bohdan B. Khomtchouk ◽  
Wolfgang Nonner
Keyword(s):  
Codon Usage ◽  
Gaussian Distribution ◽  
Large Set ◽  
Empirical Relations ◽  
A Genome ◽  
Wide Range ◽  
Protein Primary Structure ◽  
Prokaryotic Genomes ◽  
Rank Relations

AbstractDNA encodes protein primary structure using 64 different codons to specify 20 different amino acids and a stop signal. Frequencies of codon occurrence when ordered in descending sequence provide a global characterization of a genome’s preference (bias) for using the different codons of the redundant genetic code. Whereas frequency/rank relations have been described by empirical relations, here we propose a statistical model in which two different forms of codon usage co-exist in a genome. We investigate whether such a model can account for the range of codon usages observed in a large set of genomes from different taxa. The differences in frequency/rank relations across these genomes can be expressed in a single parameter, the proportion of the two codon compartments. One compartment uses different codons with weak bias according to a Gaussian distribution of frequency, the other uses different codons with strong bias. In prokaryotic genomes both compartments appear to be present in a wide range of proportions, whereas in eukaryotic genomes the compartment with Gaussian distribution tends to dominate. Codon frequencies that are Gaussian-distributed suggest that many evolutionary conditions are involved in shaping weakly-biased codon usage, whereas strong bias in codon usage suggests dominance of few evolutionary conditions.

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